Born at Frankfurt am Main, Weismann studied medicine at Göttingen, graduating in 1856. He took several temporary jobs before joining the medical faculty of the University of Freiburg in 1863.

In his early work Weismann made much use of the microscope, but failing eyesight forced him to abandon microscopy for theoretical biology. His microscopic observations, especially those on the origin of the germ cells of hydrozoans, were nevertheless put to good use in the formulation of his theory of the continuity of the germ plasm, which he published in 1886 (English translation, 1893; The Germ-Plasm: A Theory of Heredity). Weismann had noted that germ cells can be distinguished from somatic cells early in embryonic development, and from this he visualized the protoplasm of the germ cell (germ plasm) as being passed on unchanged through the generations and therefore responsible for inheritance. Although the body might be modified by environmental effects, the germ plasm – well protected within it – could not be. This insulation of the germ plasm from environmental influences – the so-called Weismann barrier – is one of the fundamental tenets of modern Darwinian theory. Weismann himself argued strongly against the Lamarckian theory of the inheritance of acquired characteristics. His publication Studies in the Theory of Descent (1882) contained a preface by Darwin.

Weismann closely followed Edouard van Beneden's work on meiosis (reduction division of cells) and arrived at the correct explanation for this process – that a reduction division is necessary to prevent chromosome numbers doubling at fertilization. Weismann became director of the new museum and zoological institute built at Freiburg and remained at the university until his retirement in 1912.